Suggestion: should have some kind of warning or put it as the default, or at least a progress bar that shows the progress of duplicate checking. and duplicates should be real duplicates. byte-for-byte same data and meta data. Two pieces of notes with the same title yet different time should be recognized as two distinct notes.

There's just one question here: why exactly are you expecting from a note-taking program functionality of a general-purpose database and want to impose your semantic over semantic that's built in to the program?